It seems I'm in the same boat.
Trying to get Zelda 1 FDS in the official VC (as that seems to be the only way to get the mic function for Pols Voice, via [L+R, Y] to switch controllers, then use the 3DS mic). For whatever reason, the official JP Zelda 1 title is the Famicom rerelease rather than the FDS original, so I lose the FDS sound on that route. All unofficial emulation I know of fails to provide mic function (nesDS has a mic button but it doesn't seem to work). I can inject the original FDS game into the official VC, but there's no way to flip disk sides, so you can't get past the title screen.
I'm guessing the .patch files modify either the ROM or the VC loader to work around the disk switching matter.
Any ideas?